251
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Seah C, Brennand KJ. If there is not one cure for schizophrenia, there may be many. NPJ SCHIZOPHRENIA 2020; 6:11. [PMID: 32313122 PMCID: PMC7170875 DOI: 10.1038/s41537-020-0101-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 02/28/2020] [Indexed: 11/24/2022]
Affiliation(s)
- Carina Seah
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kristen J Brennand
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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252
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Fernando MB, Ahfeldt T, Brennand KJ. Modeling the complex genetic architectures of brain disease. Nat Genet 2020; 52:363-369. [PMID: 32203467 PMCID: PMC7909729 DOI: 10.1038/s41588-020-0596-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 02/21/2020] [Indexed: 12/12/2022]
Abstract
The genetic architecture of each individual comprises common and rare variants that, acting alone and in combination, confer risk of disease. The cell-type-specific and/or context-dependent functional consequences of the risk variants linked to brain disease must be resolved. Coupling human induced pluripotent stem cell (hiPSC)-based technology with CRISPR-based genome engineering facilitates precise isogenic comparisons of variants across genetic backgrounds. Although functional-validation studies are typically performed on one variant in isolation and in one cell type at a time, complex genetic diseases require multiplexed gene perturbations to interrogate combinations of genes and resolve physiologically relevant disease biology. Our aim is to discuss advances at the intersection of genomics, hiPSCs and CRISPR. A better understanding of the molecular mechanisms underlying disease risk will improve genetic diagnosis, drive phenotypic drug discovery and pave the way toward precision medicine.
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Affiliation(s)
- Michael B Fernando
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Alper Neural Stem Cell Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tim Ahfeldt
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Alper Neural Stem Cell Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kristen J Brennand
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Alper Neural Stem Cell Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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253
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Abstract
The spread of protein aggregates during disease progression is a common theme underlying many neurodegenerative diseases. The microtubule-associated protein tau (MAPT) plays a central role in the pathogenesis of several forms of dementia known as tauopathies, including Alzheimer’s disease (AD), frontotemporal dementia (FTD) and chronic traumatic encephalopathy (CTE)1. Progression of these diseases is characterized by the sequential spread and deposition of protein aggregates in a predictable pattern that correlates with clinical severity2. This observation and complementary experimental studies3,4 have suggested that tau can spread in a prion-like manner by passing to naïve cells where it templates misfolding and aggregation. However, while tau propagation has been extensively studied, the underlying cellular mechanisms remain poorly understood. Here we show that the low-density lipoprotein (LDL) receptor-related protein 1 (LRP1) controls tau endocytosis and subsequent spread. Knockdown of LRP1 significantly reduced tau uptake in H4 neuroglioma cells and iPS-derived neurons. The interaction between tau and LRP1 is mediated by lysine residues in the microtubule binding repeat region of tau. Furthermore, we find that downregulation of LRP1 in an in vivo mouse model of tau spread effectively reduced tau propagation between neurons. Our results identify LRP1 as a key regulator of tau spread in the brain and, thus, as a novel target for diseases of tau spread and aggregation.
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254
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Herholt A, Galinski S, Geyer PE, Rossner MJ, Wehr MC. Multiparametric Assays for Accelerating Early Drug Discovery. Trends Pharmacol Sci 2020; 41:318-335. [PMID: 32223968 DOI: 10.1016/j.tips.2020.02.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 02/21/2020] [Accepted: 02/27/2020] [Indexed: 02/07/2023]
Abstract
Drug discovery campaigns are hampered by substantial attrition rates largely due to a lack of efficacy and safety reasons associated with candidate drugs. This is true in particular for genetically complex diseases, where insufficient knowledge of the modulatory actions of candidate drugs on targets and entire target pathways further adds to the problem of attrition. To better profile compound actions on targets, potential off-targets, and disease-linked pathways, new innovative technologies need to be developed that can elucidate the complex cellular signaling networks in health and disease. Here, we discuss progress in genetically encoded multiparametric assays and mass spectrometry (MS)-based proteomics, which both represent promising toolkits to profile multifactorial actions of drug candidates in disease-relevant cellular systems to promote drug discovery and personalized medicine.
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Affiliation(s)
- Alexander Herholt
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany; Systasy Bioscience GmbH, Balanstr. 6, 81669, Munich, Germany
| | - Sabrina Galinski
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany; Systasy Bioscience GmbH, Balanstr. 6, 81669, Munich, Germany
| | - Philipp E Geyer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Planegg, Germany; NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark; OmicEra Diagnostics GmbH, Am Klopferspitz 19, 82152, Planegg, Germany
| | - Moritz J Rossner
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany
| | - Michael C Wehr
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany; Systasy Bioscience GmbH, Balanstr. 6, 81669, Munich, Germany.
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255
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Sandoval A, Elahi H, Ploski JE. Genetically Engineering the Nervous System with CRISPR-Cas. eNeuro 2020; 7:ENEURO.0419-19.2020. [PMID: 32098761 PMCID: PMC7096538 DOI: 10.1523/eneuro.0419-19.2020] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 02/10/2020] [Accepted: 02/11/2020] [Indexed: 12/16/2022] Open
Abstract
The multitude of neuronal subtypes and extensive interconnectivity of the mammalian brain presents a substantial challenge to those seeking to decipher its functions. While the molecular mechanisms of several neuronal functions remain poorly characterized, advances in next-generation sequencing (NGS) and gene-editing technology have begun to close this gap. The clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein (CRISPR-Cas) system has emerged as a powerful genetic tool capable of manipulating the genome of essentially any organism and cell type. This technology has advanced our understanding of complex neurologic diseases by enabling the rapid generation of novel, disease-relevant in vitro and transgenic animal models. In this review, we discuss recent developments in the rapidly accelerating field of CRISPR-mediated genome engineering. We begin with an overview of the canonical function of the CRISPR platform, followed by a functional review of its many adaptations, with an emphasis on its applications for genetic interrogation of the normal and diseased nervous system. Additionally, we discuss limitations of the CRISPR editing system and suggest how future modifications to existing platforms may advance our understanding of the brain.
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Affiliation(s)
- Alfredo Sandoval
- School of Behavioral and Brain Sciences and the Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX 75080
| | - Hajira Elahi
- School of Behavioral and Brain Sciences and the Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX 75080
| | - Jonathan E Ploski
- School of Behavioral and Brain Sciences and the Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX 75080
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256
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Guo X, Aviles G, Liu Y, Tian R, Unger BA, Lin YHT, Wiita AP, Xu K, Correia MA, Kampmann M. Mitochondrial stress is relayed to the cytosol by an OMA1-DELE1-HRI pathway. Nature 2020; 579:427-432. [PMID: 32132707 PMCID: PMC7147832 DOI: 10.1038/s41586-020-2078-2] [Citation(s) in RCA: 328] [Impact Index Per Article: 82.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 02/03/2020] [Indexed: 12/12/2022]
Abstract
In mammalian cells, mitochondrial dysfunction triggers the integrated stress response (ISR), in which eIF2α phosphorylation induces the transcription factor ATF41-3. However, how mitochondrial stress is relayed to ATF4 is unknown. We found that HRI is the eIF2α kinase necessary and sufficient for this relay. In a genome-wide CRISPRi screen, we identified factors upstream of HRI: OMA1, a mitochondrial stress-activated protease, and DELE1, a little-characterized protein we found to be associated with the inner mitochondrial membrane. Mitochondrial stress stimulates OMA1-dependent cleavage of DELE1, leading to its accumulation in the cytosol, where it interacts with HRI and activates its eIF2α kinase activity. Additionally, DELE1 is required for ATF4 translation downstream of eIF2α phosphorylation. Blockade of the OMA1-DELE1-HRI pathway triggers an alternative response inducing specific molecular chaperones. Therefore, this pathway is a potential therapeutic target enabling fine-tuning of the ISR for beneficial outcomes in diseases involving mitochondrial dysfunction.
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Affiliation(s)
- Xiaoyan Guo
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Giovanni Aviles
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Yi Liu
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Ruilin Tian
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA.,Biophysics Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Bret A Unger
- Chan Zuckerberg Biohub, San Francisco, CA, USA.,Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Yu-Hsiu T Lin
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Arun P Wiita
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Ke Xu
- Chan Zuckerberg Biohub, San Francisco, CA, USA.,Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - M Almira Correia
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.,The Liver Center, University of California, San Francisco, San Francisco, CA, USA
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, USA. .,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
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257
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Jost M, Santos DA, Saunders RA, Horlbeck MA, Hawkins JS, Scaria SM, Norman TM, Hussmann JA, Liem CR, Gross CA, Weissman JS. Titrating gene expression using libraries of systematically attenuated CRISPR guide RNAs. Nat Biotechnol 2020; 38:355-364. [PMID: 31932729 PMCID: PMC7065968 DOI: 10.1038/s41587-019-0387-5] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 12/05/2019] [Indexed: 02/07/2023]
Abstract
A lack of tools to precisely control gene expression has limited our ability to evaluate relationships between expression levels and phenotypes. Here, we describe an approach to titrate expression of human genes using CRISPR interference and series of single-guide RNAs (sgRNAs) with systematically modulated activities. We used large-scale measurements across multiple cell models to characterize activities of sgRNAs containing mismatches to their target sites and derived rules governing mismatched sgRNA activity using deep learning. These rules enabled us to synthesize a compact sgRNA library to titrate expression of ~2,400 genes essential for robust cell growth and to construct an in silico sgRNA library spanning the human genome. Staging cells along a continuum of gene expression levels combined with single-cell RNA-seq readout revealed sharp transitions in cellular behaviors at gene-specific expression thresholds. Our work provides a general tool to control gene expression, with applications ranging from tuning biochemical pathways to identifying suppressors for diseases of dysregulated gene expression.
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Affiliation(s)
- Marco Jost
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Daniel A Santos
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Reuben A Saunders
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Max A Horlbeck
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA, USA
| | - John S Hawkins
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Sonia M Scaria
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Thomas M Norman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA, USA
- Computational & Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jeffrey A Hussmann
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Christina R Liem
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Carol A Gross
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA.
- California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA, USA.
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258
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Chen JJ, Nathaniel DL, Raghavan P, Nelson M, Tian R, Tse E, Hong JY, See SK, Mok SA, Hein MY, Southworth DR, Grinberg LT, Gestwicki JE, Leonetti MD, Kampmann M. Compromised function of the ESCRT pathway promotes endolysosomal escape of tau seeds and propagation of tau aggregation. J Biol Chem 2019; 294:18952-18966. [PMID: 31578281 PMCID: PMC6916486 DOI: 10.1074/jbc.ra119.009432] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 09/26/2019] [Indexed: 12/22/2022] Open
Abstract
Intercellular propagation of protein aggregation is emerging as a key mechanism in the progression of several neurodegenerative diseases, including Alzheimer's disease and frontotemporal dementia (FTD). However, we lack a systematic understanding of the cellular pathways controlling prion-like propagation of aggregation. To uncover such pathways, here we performed CRISPR interference (CRISPRi) screens in a human cell-based model of propagation of tau aggregation monitored by FRET. Our screens uncovered that knockdown of several components of the endosomal sorting complexes required for transport (ESCRT) machinery, including charged multivesicular body protein 6 (CHMP6), or CHMP2A in combination with CHMP2B (whose gene is linked to familial FTD), promote propagation of tau aggregation. We found that knocking down the genes encoding these proteins also causes damage to endolysosomal membranes, consistent with a role for the ESCRT pathway in endolysosomal membrane repair. Leakiness of the endolysosomal compartment significantly enhanced prion-like propagation of tau aggregation, likely by making tau seeds more available to pools of cytoplasmic tau. Together, these findings suggest that endolysosomal escape is a critical step in tau propagation in neurodegenerative diseases.
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Affiliation(s)
- John J Chen
- Institute for Neurodegenerative Diseases, University of California, San Francisco, California 94158
| | - Diane L Nathaniel
- Institute for Neurodegenerative Diseases, University of California, San Francisco, California 94158
| | | | - Maxine Nelson
- Institute for Neurodegenerative Diseases, University of California, San Francisco, California 94158
- Biomedical Sciences Graduate Program, University of California, San Francisco, California 94158
| | - Ruilin Tian
- Institute for Neurodegenerative Diseases, University of California, San Francisco, California 94158
- Biophysics Graduate Program, University of California, San Francisco, California 94158
| | - Eric Tse
- Institute for Neurodegenerative Diseases, University of California, San Francisco, California 94158
| | - Jason Y Hong
- Institute for Neurodegenerative Diseases, University of California, San Francisco, California 94158
| | - Stephanie K See
- Institute for Neurodegenerative Diseases, University of California, San Francisco, California 94158
- Graduate Program in Chemistry and Chemical Biology, University of California, San Francisco, California 94158
| | - Sue-Ann Mok
- Institute for Neurodegenerative Diseases, University of California, San Francisco, California 94158
| | - Marco Y Hein
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158
| | - Daniel R Southworth
- Institute for Neurodegenerative Diseases, University of California, San Francisco, California 94158
- Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158
| | - Lea T Grinberg
- Department of Neurology, University of California, San Francisco, California 94158
| | - Jason E Gestwicki
- Institute for Neurodegenerative Diseases, University of California, San Francisco, California 94158
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158
| | | | - Martin Kampmann
- Institute for Neurodegenerative Diseases, University of California, San Francisco, California 94158
- Chan Zuckerberg Biohub, San Francisco, California 94158
- Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158
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259
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So RWL, Chung SW, Lau HHC, Watts JJ, Gaudette E, Al-Azzawi ZAM, Bishay J, Lin LTW, Joung J, Wang X, Schmitt-Ulms G. Application of CRISPR genetic screens to investigate neurological diseases. Mol Neurodegener 2019; 14:41. [PMID: 31727120 PMCID: PMC6857349 DOI: 10.1186/s13024-019-0343-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/31/2019] [Indexed: 12/14/2022] Open
Abstract
The adoption of CRISPR-Cas9 technology for functional genetic screens has been a transformative advance. Due to its modular nature, this technology can be customized to address a myriad of questions. To date, pooled, genome-scale studies have uncovered genes responsible for survival, proliferation, drug resistance, viral susceptibility, and many other functions. The technology has even been applied to the functional interrogation of the non-coding genome. However, applications of this technology to neurological diseases remain scarce. This shortfall motivated the assembly of a review that will hopefully help researchers moving in this direction find their footing. The emphasis here will be on design considerations and concepts underlying this methodology. We will highlight groundbreaking studies in the CRISPR-Cas9 functional genetics field and discuss strengths and limitations of this technology for neurological disease applications. Finally, we will provide practical guidance on navigating the many choices that need to be made when implementing a CRISPR-Cas9 functional genetic screen for the study of neurological diseases.
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Affiliation(s)
- Raphaella W. L. So
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, Ontario M5S 1A8 Canada
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor60 Leonard Avenue, Toronto, Ontario M5T 2S8 Canada
| | - Sai Wai Chung
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, Ontario M5S 1A8 Canada
| | - Heather H. C. Lau
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, Ontario M5S 1A8 Canada
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor60 Leonard Avenue, Toronto, Ontario M5T 2S8 Canada
| | - Jeremy J. Watts
- Department of Pharmacology & Toxicology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, Ontario M5S 1A8 Canada
| | - Erin Gaudette
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, Ontario M5S 1A8 Canada
| | - Zaid A. M. Al-Azzawi
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, Ontario M5S 1A8 Canada
| | - Jossana Bishay
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, Ontario M5S 1A8 Canada
| | - Lilian Tsai-Wei Lin
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, Ontario M5S 1A8 Canada
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor60 Leonard Avenue, Toronto, Ontario M5T 2S8 Canada
| | - Julia Joung
- Departments of Biological Engineering and Brain and Cognitive Science, and McGovern Institute for Brain Research at MIT, Cambridge, MA 02139 USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Xinzhu Wang
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, Ontario M5S 1A8 Canada
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor60 Leonard Avenue, Toronto, Ontario M5T 2S8 Canada
| | - Gerold Schmitt-Ulms
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, Ontario M5S 1A8 Canada
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor60 Leonard Avenue, Toronto, Ontario M5T 2S8 Canada
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260
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Karch CM, Kao AW, Karydas A, Onanuga K, Martinez R, Argouarch A, Wang C, Huang C, Sohn PD, Bowles KR, Spina S, Silva MC, Marsh JA, Hsu S, Pugh DA, Ghoshal N, Norton J, Huang Y, Lee SE, Seeley WW, Theofilas P, Grinberg LT, Moreno F, McIlroy K, Boeve BF, Cairns NJ, Crary JF, Haggarty SJ, Ichida JK, Kosik KS, Miller BL, Gan L, Goate AM, Temple S. A Comprehensive Resource for Induced Pluripotent Stem Cells from Patients with Primary Tauopathies. Stem Cell Reports 2019; 13:939-955. [PMID: 31631020 PMCID: PMC6895712 DOI: 10.1016/j.stemcr.2019.09.006] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 09/16/2019] [Accepted: 09/17/2019] [Indexed: 12/14/2022] Open
Abstract
Primary tauopathies are characterized neuropathologically by inclusions containing abnormal forms of the microtubule-associated protein tau (MAPT) and clinically by diverse neuropsychiatric, cognitive, and motor impairments. Autosomal dominant mutations in the MAPT gene cause heterogeneous forms of frontotemporal lobar degeneration with tauopathy (FTLD-Tau). Common and rare variants in the MAPT gene increase the risk for sporadic FTLD-Tau, including progressive supranuclear palsy (PSP) and corticobasal degeneration (CBD). We generated a collection of fibroblasts from 140 MAPT mutation/risk variant carriers, PSP, CBD, and cognitively normal controls; 31 induced pluripotent stem cell (iPSC) lines from MAPT mutation carriers, non-carrier family members, and autopsy-confirmed PSP patients; 33 genome engineered iPSCs that were corrected or mutagenized; and forebrain neural progenitor cells (NPCs). Here, we present a resource of fibroblasts, iPSCs, and NPCs with comprehensive clinical histories that can be accessed by the scientific community for disease modeling and development of novel therapeutics for tauopathies. A collection of fibroblasts from 140 MAPT mutation carriers, PSP, CBD, and controls 31 iPSC lines reprogrammed from MAPT mutation carriers, PSP patients, and controls 33 iPSC lines engineered with CRISPR/Cas9 or TALENs Comprehensive resource for tauopathy modeling and discovery of novel therapeutics
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Affiliation(s)
- Celeste M Karch
- Department of Psychiatry, Washington University in St. Louis School of Medicine, 425 South Euclid Avenue, Campus Box 8134, St. Louis, MO 63110, USA.
| | - Aimee W Kao
- Division of Memory and Aging Center, Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Anna Karydas
- Division of Memory and Aging Center, Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Khadijah Onanuga
- Neural Stem Cell Institute, 1 Discovery Drive, Rensselaer, NY 12144, USA
| | - Rita Martinez
- Department of Psychiatry, Washington University in St. Louis School of Medicine, 425 South Euclid Avenue, Campus Box 8134, St. Louis, MO 63110, USA
| | - Andrea Argouarch
- Division of Memory and Aging Center, Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Chao Wang
- Gladstone Institutes of Neurological Disease, Department of Neurology, Neuroscience Graduate Program, University of California, San Francisco, CA 94158, USA
| | - Cindy Huang
- Gladstone Institutes of Neurological Disease, Department of Neurology, Neuroscience Graduate Program, University of California, San Francisco, CA 94158, USA
| | - Peter Dongmin Sohn
- Gladstone Institutes of Neurological Disease, Department of Neurology, Neuroscience Graduate Program, University of California, San Francisco, CA 94158, USA
| | - Kathryn R Bowles
- Ronald M. Loeb Center for Alzheimer's Disease, Departments of Neuroscience, Neurology and Genetics & Genomic Sciences, Icahn School of Medicine, New York, NY 10029, USA
| | - Salvatore Spina
- Division of Memory and Aging Center, Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - M Catarina Silva
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Departments of Neurology & Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Jacob A Marsh
- Department of Psychiatry, Washington University in St. Louis School of Medicine, 425 South Euclid Avenue, Campus Box 8134, St. Louis, MO 63110, USA
| | - Simon Hsu
- Department of Psychiatry, Washington University in St. Louis School of Medicine, 425 South Euclid Avenue, Campus Box 8134, St. Louis, MO 63110, USA
| | - Derian A Pugh
- Ronald M. Loeb Center for Alzheimer's Disease, Departments of Neuroscience, Neurology and Genetics & Genomic Sciences, Icahn School of Medicine, New York, NY 10029, USA
| | - Nupur Ghoshal
- Department of Neurology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Joanne Norton
- Department of Psychiatry, Washington University in St. Louis School of Medicine, 425 South Euclid Avenue, Campus Box 8134, St. Louis, MO 63110, USA
| | - Yadong Huang
- Gladstone Institutes of Neurological Disease, Department of Neurology, Neuroscience Graduate Program, University of California, San Francisco, CA 94158, USA
| | - Suzee E Lee
- Division of Memory and Aging Center, Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - William W Seeley
- Division of Memory and Aging Center, Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Panagiotis Theofilas
- Department of Pathology and Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Lea T Grinberg
- Department of Pathology and Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Fermin Moreno
- Division of Memory and Aging Center, Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kathryn McIlroy
- Neural Stem Cell Institute, 1 Discovery Drive, Rensselaer, NY 12144, USA
| | - Bradley F Boeve
- Department of Neurology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Nigel J Cairns
- Department of Neurology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - John F Crary
- Ronald M. Loeb Center for Alzheimer's Disease, Departments of Neuroscience, Neurology and Genetics & Genomic Sciences, Icahn School of Medicine, New York, NY 10029, USA; Department of Pathology, Fishberg Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Stephen J Haggarty
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Departments of Neurology & Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Justin K Ichida
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Kenneth S Kosik
- Department of Molecular Cellular and Developmental Biology, Neuroscience Research Institute, Biomolecular Science and Engineering Program, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Bruce L Miller
- Division of Memory and Aging Center, Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Li Gan
- Gladstone Institutes of Neurological Disease, Department of Neurology, Neuroscience Graduate Program, University of California, San Francisco, CA 94158, USA
| | - Alison M Goate
- Ronald M. Loeb Center for Alzheimer's Disease, Departments of Neuroscience, Neurology and Genetics & Genomic Sciences, Icahn School of Medicine, New York, NY 10029, USA
| | - Sally Temple
- Neural Stem Cell Institute, 1 Discovery Drive, Rensselaer, NY 12144, USA.
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Convergence in neuropsychiatric research. Nat Methods 2019; 16:961-964. [PMID: 31537909 DOI: 10.1038/s41592-019-0578-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Screen time: studying gene function in iPSCs. Nat Rev Neurosci 2019; 20:573. [PMID: 31467449 DOI: 10.1038/s41583-019-0217-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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